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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

2b4t

2.500 Å

X-ray

2005-09-26

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glyceraldehyde-3-phosphate dehydrogenase
ID:Q8T6B1_PLAFA
AC:Q8T6B1
Organism:Plasmodium falciparum
Reign:Eukaryota
TaxID:5833
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
O100 %


Ligand binding site composition:

B-Factor:54.076
Number of residues:15
Including
Standard Amino Acids: 13
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors: NAD
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.717752.625

% Hydrophobic% Polar
33.6366.37
According to VolSite

Ligand :
2b4t_1 Structure
HET Code: AES
Formula: C8H11FNO2S
Molecular weight: 204.242 g/mol
DrugBank ID: DB07347
Buried Surface Area:47.17 %
Polar Surface area: 70.16 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 1
Rings: 1
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
13.974317.400212.3354


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
C2CBTHR- 1834.330Hydrophobic
C3CBALA- 1844.140Hydrophobic
C5CBASN- 1854.10Hydrophobic
FC2DNAD- 5014.250Hydrophobic
C1C2DNAD- 5013.540Hydrophobic
C5C3DNAD- 5014.050Hydrophobic
O2SO2DNAD- 5012.66149.99H-Bond
(Protein Donor)
N8O1ANAD- 5012.61169.09H-Bond
(Ligand Donor)
N8O1ANAD- 5012.610Ionic
(Ligand Cationic)